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Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 277 50mM Mes, 1.4M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.663 α = 90 b = 51.842 β = 90 c = 131.475 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.827 65.738 99.8 0.095 0.103 0.038 13.9 7.2 27881 27881
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.93 98.6 0.47 1.6 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DB1 1.83 48.27 26427 1394 99.76 0.1918 0.1904 0.1989 0.2171 0.2245 RANDOM 19.969
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.82 -0.53 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 18.969 r_dihedral_angle_3_deg 15.675 r_dihedral_angle_1_deg 7.288 r_angle_refined_deg 2.244 r_angle_other_deg 1.057 r_chiral_restr 0.147 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 18.969 r_dihedral_angle_3_deg 15.675 r_dihedral_angle_1_deg 7.288 r_angle_refined_deg 2.244 r_angle_other_deg 1.057 r_chiral_restr 0.147 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2027 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 36
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction